oligo file - two barcodes / indices

Commands in mothur
1

Hi,

I just have a question about writing the oligo file.

For my MiSeq run, a dual indexing system was used (two indices (or barcodes) per sample), one index in one adapter and one in the other: index i5 and index i7.

How should these be written in the oligo file? Will this work:

forward GTGCCAGCMGCCGCGGTAA
reverse GGACTACHVGGGTWTCTAAT
barcode TAAGGCGA-TAGATCGC APM_C01_FOP_2014_001
barcode TAAGGCGA-CTCTCTAT APM_C01_FOP_2014_002
barcode TAAGGCGA-TATCCTCT APM_C01_FOP_2014_003
.
.

Many thanks for any suggestions,

Julia

2

Here’s a link to mothur’s oligos file setup, http://www.mothur.org/wiki/Oligos_File.